Package pl.krakow.cmuj.bioinformatics.jellipse

Provides main application networking, file-handling and GUI support.

See:
Description

Interface Summary

ColorScheme	Interface allowing switching between predefined color schemes.
Plottable	Common functions for all properties that can be represented in a 2D plot.
Screenshottable

Class Summary

About	Displays a window with a short conventional information about the program.
AbsDeviation	Enables plotting the absolute value of the difference between the Ln of the radius of curvature of the current structure (observable) and the value of the parameter obtained analyzing model peptides.
AvgDihedralAngle	Enables plotting averaged dihedral angle between consecutive peptide bond planes computed along the whole polypeptide chain.
ChainChooser	If there is more than one chain in the PDB file, enables user to choose.
Deviation	Enables plotting the difference between the log,sub>n of radius of curvature of the current structure (observable) and the value of the parameter obtained analyzing model peptides.
FFilter	A convenient implementation of FileFilter that allow context dialog searches of files.
jEllipse	Main application class serving all grqphic data representations.
LnCurvature	Enables plotting natural logarithm of the radius of the local curvature computed along the whole polypeptide chain.
LnRvsVPlot
PdbFetcher	Loads PDB file content via http protocol from RCSB or from a local file.
PdbFile	String operations' implementations are dirty and require more study on regexps, although they work and are quite fast.
PinkBlue	Pastel, a bit synthetic color scheme.
PlotRenderer
Quickinfo	Window with hints on navigation.
RamachandranMap
RedGreen	Fresh or even garish color scheme.
References	Window with related publications.
ScreenShot
StructureRenderer
Surface	General-purpose drawing (plotting area).
SwingWorker	This is the 3rd version of SwingWorker, an abstract class that yousubclass to perform GUI-related work in a dedicated thread.
SwingWorker.ThreadVar	Class to maintain reference to current worker thread under separate synchronization control.

Package pl.krakow.cmuj.bioinformatics.jellipse Description

Provides main application networking, file-handling and GUI support.
Main project features:

• ultimately task-oriented: intented to be a complete presentation of a particular model,
• no use of any third-party bioinformatics software,
• emphasis on graphical presentation of data,
• extensive use of java 1.5 novelties.

Package Specification

The package application is strongly dependent on the JOGL - Java bindings for OpenGL. There is no other third-party code involved.

• JOGL homepage

Related Documentation

For short summary of the project please see:

• Overview [6 pages pdf]

For detailed description of approach and methodology involved please refer to:

• Roterman I., 1995, Modelling the optimal simulation path in the peptide chain folding - Studies based on geometry of alanine heptapeptide J Theor Biol, 177, 283-288


• Roterman I., 1995, The geomerical analysis of peptide backbone structure and its local deformations Biochimie, 77, 204-216


• Leluk, J. et al, 2003, Search for structural similarity in proteins Bioinformatics 19, 117-124 [here the present app was introduced as VeaR]


• Brylinski, M. et al, 2004, Limited conformational space for early-stage protein folding simulation Bioinformatics 20, 199-205

Project www

Homepage

Author

The only author of the software is Marek Kochanczyk (kochanczyk[monkeytail]corcoran.if.uj.edu.pl), MSc student of the Dept. of Physics, Astronomy and Computer Science, Jagiellonian Univeristy, Krakow, Poland and associated student at the Dept. of Bioinformatics and Telemedicine of Medical College, Jagiellonian University, Krakow, Poland.